Monday, March 26, 2012

You blew it last week because you didn't follow instructions. It's not going to get any easier. This week you have to identify the molecule using TWO different common names AND name the Nobel Prize winner most closely associated with this molecule.

Remember, you need THREE answers or you can't win!

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is Vitamin B12, also known as cobalamin. The Nobel Laureate is Dorothy Crowfoot Hodgkin. This week's winners are John Runnels and Raul A. Félix de Sousa. Contact me by email to set up a time.

Thursday, March 22, 2012

The predicted mutation rate in humans is thought to be about 130 mutations per generation or 10-10 per nucleotide per generation [Mutation Rates]. About 120 (>90%)of these new mutations occur in males, mostly during spermatogenesis. Only about 10 mutations are contributed by females. These values are based on what we know about the biochemistry of DNA replication and repair.

The evidence from evolution was consistent with this calculation. Nachman and Crowell (2000), for example, calculated that the accumulation of mutations in 18 pseudogenes from humans and chimpanzees yielded a value of 175 mutations per generation.

Up until recently it wasn't possible to get a direct measurement of the mutation rate but I addressed some of the attempts in November 2010: Human Mutation Rates. In that posting I discussed two experimental results that yielded estimates of the mutation rates in humans.

Recently there have been two attempts to verify this calculation. In one, the Y chromosomes of two men separated by 13 generations in a paternal lineage from a common male ancestor were sequenced. The differences correspond to a mutation rate of 0.75 × 10-10 per generation, or almost the same as theory predicts. This is based on the fact that if most mutations are nearly neutral (they are) then the rate of fixation by random genetic drift should be the same as the mutation rate.

The other study, by Roach et al. (2010), compared the genome sequences of two offspring and their parents. By adding up all the differences in the offspring they arrived at an estimate of 70 mutations in the offspring instead of the expected 130. This is half the expected value but the study is fraught with potential artifacts and it's best not to make a big deal of this discrepancy.

Now there's another paper that sequenced two sets of parents and a child (Conrad et al., 2011). You might think that the calculation is easy because all you have to do is count the number of new alleles in the child. But this doesn't work because you have to account for somatic mutations that arose in the tissue culture cells lines that are being used as a source of DNA. These can be eliminated by comparing the sequence with fresh DNA samples directly from the parents and child. In addition to false positives, you have to allow for some false negatives.

I don't understand all the mathematical manipulations but they are probably trustworthy. (Some of it was done by Reed Cartwright of Panda's Thumb.) The final estimates are 60 mutations in one of the children and 50 in the other. Both of these values are lower than the calculated rate and when you combine them with earlier results, it's beginning to look like the actual mutation rate is about half of the calculated value based on biochemistry. This could easily be due to a two-fold error in our estimate of repair efficiency. It could be that instead of repairing only 99/100 sites of damage the actual repair machinery fixes 199/200 damaged sites, for example.

The surprising result is that 92% of the new mutations in one of the children comes from the father but in the other family only 32% of the mutations were paternal. We expect that most of the mutations will occur during spermatogenesis so that part is not surprising. What's surprising is that in one case the majority come from the mother.

I suspect that this is an artifact of some kind, or a statistical outlier. The authors, however, take this as evidence of natural variation in male and female mutation rates. I'd like to see the estimates for other children of the same family in order to see if the result is reproducible.

I subscribe to New Scientist. Many years ago, I decided that it was the best of the popular science magazines—better than Scientific American, National Geographic, SEED (now defunct), and Discover. Recently, however, I been having second thoughts as the quality of the articles deteriorates and more and more pseudoscience and wrong science is making its way into the magazine. The issue of March 17-23, 2011—The God Issue—is the last straw. This is no longer a science magazine.

It's not because the topic is out-of-bounds. Quite the contrary, I think it's perfectly appropriate to address the conflict between science and religion. There's even a good article in there; it's the one by Victor Stenger. Stenger argues convincingly that science conflicts with the existence of all personal gods. It's possibly compatible with a strictly deist god but nobody believes in such a god.

The problem is with all the other articles which are accommodationist to various degrees. Several of them flatly contradict science (and common sense). One of them (by Alain de Botton) advocates that atheists adopt some of the practices of religion as if religion has a monopoly on being nice.

You only have to read the editorial to see how bad things have become ....

"GIVE me the child until he is seven, and I will show you the man." This Jesuit maxim epitomises how many of us perceive religion: as something that must be imprinted on young minds.

The new science of religion begs to differ. Children are born primed to see god at work all around them and don't need to be indoctrinated to believe in him (see "The God issue: We are all born believers").

This is just one of many recent findings that are challenging standard critiques of religious belief. As we learn more about religion's biological roots, it is becoming clear that secularists are often tilting at windmills and need to rethink.

Another such finding is that belief in a god or gods does appear to encourage people to be nice to one another. Humans clearly don't need religion to be moral, but it helps (see "The God issue: Religion is the key to civilisation").

An interesting corollary of this is a deeply held mistrust of atheists (see "In atheists we distrust"). In fact, atheists might consider themselves as unrecognised victims of discrimination. In a recent opinion poll, Americans identified atheists as the group they would most disapprove of their children marrying and the one least likely to share their own vision of American society. Self-declared atheists are now the only sizeable minority group considered unelectable as president.

Such antipathy poses a dilemma for opponents of religion, and may explain why "militant atheism" has failed to make headway.

Secularists would also do well to recognise the distinction between the "popular religion" that comes easily to people's minds and the convoluted intellectual gymnastics that is theology. Attacking the latter is easy but will do little to undermine religion's grip (see "The God issue: Science won't loosen religion's grip").

This is not an apologia for god. Religious claims still wither under rational scrutiny and deserve no special place in public life. But it is a call for those who aspire to a secular society to approach it rationally - which means making more effort to understand what they are dealing with. Religion is deeply etched in human nature and cannot be dismissed as a product of ignorance, indoctrination or stupidity. Until secularists recognise that, they are fighting a losing battle.

The editors seem to have been completely bamboozled by the article entitled Born Believers. The author is Justin L. Barrett of Fullier Theologial Seminary in Pasadena, California (USA). Barrett argues ....

Drawing upon research in developmental psychology, cognitive anthropology and particularly the cognitive science of religion, I argue that religion comes nearly as naturally to us as language. The vast majority of humans are "born believers", naturally inclined to find religious claims and explanations attractive and easily acquired, and to attain fluency in using them. This attraction to religion is an evolutionary by-product of our ordinary cognitive equipment, and while it tells us nothing about the truth or otherwise of religious claims it does help us see religion in an interesting new light.

Barrett quotes a few studies in support of his claim but those studies don't really say what he thinks they say. It makes no sense to say that young children find religious claims and expectations attractive unless they have heard these explanations from adults.

I don't remember a time in my childhood when I spontaneously created a supernatural being who expected me to behave in certain ways. I never saw any evidence that my children needed to create gods and I don't see any evidence that my two-year-old granddaughter needs to imagine sky daddies in order to understand the world around her.

There are millions of children in Europe who are growing up as second and third generation atheists and I can't imagine that their parents are upset because the children are turning out to be "born believers." The idea is ridiculous. It could only come from a culture where young children are being constantly brainwashed by stories about gods. There's no such thing as an innate attraction to religion in a culture with no religion in the first place.

Oh, and one other thing, it's not true that belief in one of the gods makes you a nicer person. If that were true then America would be one of the kindest, nicest, societies among all Western industrialized nations. And Saudi Arabia would take the prize for the nicest society in the world. And you sure as hell wouldn't want to live in evil, crime-ridden Sweden or Holland.

March 24th is a landmark date for Washington, D.C. Thousands will converge on the world’s leading capital city to celebrate the crowning human virtue of reason.

How have we come to the point where reason needs a rally to defend it? To base your life on reason means to base it on evidence and logic. Evidence is the only way we know to discover what’s true about the real world. Logic is how we deduce the consequences that follow from evidence. Who could be against either? Alas, plenty of people, which is why we need the Reason Rally.

I agree with Dawkins. "Reason" and rationality is what we should be promoting. If we are successful, then religion will disappear and atheism will be the default position. As Dawkins puts it in The God Delusion, the real battle is between rationalism and superstition or between reason and superstition.

Dawkins has a series of videos called The Enemies of Reason. They are promoted as: "Professor Richard Dawkins confronts the epidemic of irrational, superstitious thinking with logic, observation and evidence - in other words, through reason." Here's the episode on superstitious beliefs in health and medicine.

It's obvious that anyone who opposes vaccination and/or promotes alternative medicine is an enemy of reason. It's difficult to imagine how such a person could be invited to speak at the Reason Rally in Washington, right?

It's because some of the organizers of the Reason Rally do not agree with Richard Dawkins. They see this event as an atheist rally and the speakers are being invited because they are prominent atheists, not necessarily rationalists. Hemant Mehta of Friendly Atheist is one of those people [Plan Your Own Reason Rally and Then Tell Me How It Goes].

Look, the organizers spent a long time listening to the suggestions of dozens of people (representing tens of thousands of atheists) regarding who should speak at the Rally. They did everything in their power to contact all the “big names” that people said they wanted to hear at the Rally. They rustled up and managed the hundreds of thousands of dollars in funding needed to put on an event of this magnitude. They got every major organization in our movement to work together to make this work — and that’s not an easy thing to do. They had to deal with the speakers complaining about their prominence on our website (yep, it happened).

Just about everyone believes in something irrational. Including atheists. So, yes, you’re going to hear people at the Rally who hold ideas we think are completely unreasonable. Maybe even harmful.

If we got rid of every speaker who held an irrational belief, there would be no one left on that stage.

So deal with it.

I’m not saying you shouldn’t call them out where they’re wrong. Have at it. I did it, too. In many cases, they deserve it. But to suggest the organizers are at fault for inviting really famous atheists who hold some view you don’t agree with is absurd. Almost as ridiculous as faulting them for accepting a greeting from a sitting U.S. senator who stands to lose a lot more than he’ll gain for addressing our crowd.

This is going to be confusing. Who's right? Is this a Reason Rally as Dawkins and PZ Myers think or is it an Atheist Rally as Hemant believes?

Monday, March 19, 2012

I was searching through some old posts today and I came across I Rank Number One on Google from October 2007. The idea was to come up with five words or phrases where Google would return something by you at the top of the page.

Back then I picked ...

Larry Moran

Sandwalk

Three Domain Hypothesis

adaptationist-pluralist

is there a genetic component to intelligence

All five of them worked in 2007 but today the last one has Sandwalk in 4th position. The list that works today is ....

Larry Moran

Sandwalk

Three Domain Hypothesis

adaptationist-pluralist

random genetic drift

How easy is this? Can every blogger come up with a list where they rank number one on the Google search? I tried it with a few blog names and it always seems to work. The names of some bloggers don't always work. We already know about a more famous "John Wilkins" for example and "Paul Myers" doesn't even mention the Pharyngula blogger in the top ten!1

I'm giving a lecture tomorrow on the Three Domain Hypothesis and why it is no longer valid. I still have the top three hits for this topic on Google. In case you've forgotten, you can read about it at: Theme: The Three Domain Hypothesis.

First, there's the initiation stage when a ribosome binds to the initiation codon in messenger RNA (mRNA) and the translation initiation complex forms by recruiting additional components.

Second, there's the elongation stage when the elongation complex moves along the mRNA translating the coding region and producing a polypeptide chain. The elongation rate is relatively constant but from time to time the elongation complex pauses at particular sites that are difficult to translate.

Finally, the elongation complex encounters a termination site where it disassembles and the ribosome with its various factors is released from the mRNA.

Richard Dawkins created a bit of a stir among the theists by claiming that he is an African ape.

Someone named Vasko Kohlmayer was partularly upset so he wrote up a "rebuttal" for the Moonie newspaper The Washington Times: Is Richard Dawkins an Ape?.

I don't much care about the opinions of theists like Vasko Kohlmayer because they have an obvious agenda. Scientific arguments are meaningless to them.

But I do care about the opinions of other scientists and philosophers. Jerry Coyne explains why we are apes and why it's not a good idea to say that people living in Oxford or Chicago are African apes [Washington Times denies that Richard Dawkins is an ape]. I agree with Jerry.

Chimpanzees are apes. Gorillas are apes, as are bonobos, orangutans, and gibbons. We routinely differentiate the "great apes" from the "lesser apes", where the latter are gibbons and siamangs. Humans are not apes. Humans are hominoids, and all hominoids are anthropoids. So are Old World monkeys like baboons and New World monkeys like marmosets. All of us anthropoids. But humans aren't monkeys.

I don't agree with this distinction. There's nothing to be gained by saying that our closest relatives are apes but we aren't.

It is not possible to stem the tide of linguistic change, as the Académie Française has found out repeatedly. If experts can redefine terms influentially, then there is nothing wrong with that so long as it doesn’t confuse the experts. Using paraphyletic terms (that is, group names that denote what is left of the group once a subset has been removed) is a Very Bad Idea that hangs on in science, but it need not hang on in folk usage. And there’s nothing wrong with saying “humans are apes”, because, on the best construal of what those terms denote, they are.

Neil Shubin’s excellent book Your Inner Fish makes a similar point. Where once a “fish” was anything that lived in water (including swans, geese, alligators and crocodiles, whales, and water snakes), it came to mean a vertebrate that had gills and fins and scales. Shubin shows how the Gnathostomes (jawed fishes) includes land vertebrates, including mammals and ultimately us, as well. Language can change…

The last few challenges have been too easy so I'm going to make this week's molecule a bit more difficult. Not only do you have to identify the molecule but you also have to identify each of the four residues that are sugar derivatives. What is the molecule in blue and what are the other three sugary-looking residues?

Be sure to give a complete unambiguous name—that means getting the stereochemistry correct.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch. I'll be setting up a lunch for this Thursday so expect an email message. If I owe you a lunch, it wouldn't hurt to remind me in case I forget you.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside GM2. The residues are N-acetyl-α-neuraminic acid (blue), N-acetyl-β-D-galactosamide, β-D-galactose, and β-D-glucose (left to right). You were asked to be specific in naming the sugar residues. Several people got the molecule correct but nobody named the sugar residues in a completely unambiguous manner, although the correct names are implied in the formal name of the molecule. There is no winner this week.

Sunday, March 18, 2012

A lot of people are going to Washington next Saturday to stand1 near the reflecting pool for eight hours listening to short speeches and videos during the Reason Rally.

One of the speakers will be PZ Myers and he is rightly upset about some of the other speakers who don't exactly fit the criterion of "reason." Read what he has to say about Senator Tom Harkin and Bill Maher [The Reason Rally ought to have some standards].

Was Deepak Chopra busy on 24 March? Did Oprah have a hair appointment? Maybe it’s not too late to sign up John Edward — he could channel Ingersoll and Russell and Sagan for us, although of course we’d have to be content with him guessing at their words one letter at a time.

So what's the point of having a "Reason Rally" if you schedule talks from known kooks who oppose reason?

I suspect that a lot of people will be wandering off to look at the cherry blossoms behind the Jefferson Memorial. I hope the size of the crowd isn't an embarrassment.

You can buy a ticket for the seating area in front of the stage if you're willing to pay $500, $1000, or $5000 [VIP Seating].

Friday, March 16, 2012

Shame on the Human Genome Organization (HUGO). It has awarded a prestigious prize (US $10,000) to John Mattick, director of the Centre for Molecular Biology and Biotechnology at the University of Queensland in Brisbane, Australia. Here's the report from the Sydney Morning Herald.

Making something of junk earns geneticist top award

WHEN Sydney geneticist John Mattick suggested junk DNA was anything but rubbish he was challenging an assumption that had underpinned genetics for 50 years.

''The ideas I put forward 10 years ago were quite radical but I thought I was right,'' Professor Mattick said.

He was. And tomorrow he will become the first Australian honoured with the Chen Award for distinguished academic achievement in human genetic and genomic research, awarded by the Human Genome Organisation.

For decades after James Watson and Francis Crick discovered DNA was a double helix, scientists believed most genes were the written instructions for proteins, the building blocks of all body processes. The assumption was true for bacteria but not complex organisms like humans, said Professor Mattick, the new executive director of the Garvan Institute.

In humans, more than 95 per cent of the genome contains billions of letters that do not make proteins, called non-coding DNA. ''When people bumped into all this DNA that didn't make proteins they thought it must be junk,'' he said. But Professor Mattick felt it was unlikely that useless material would survive hundreds of millions of years of evolution.

He found that the non-protein-coding sections of DNA had a function, to produce RNA.

"The obvious and very exciting possibility was that there is another layer of information being expressed by the genome - that the non-coding RNAs form a massive and previously unrecognised regulatory network that controls human development.''

Many scientists now believe this RNA is the basis of the brain's plasticity and learning, and may hold the secret to understanding many complex diseases.

Thursday, March 15, 2012

Today is the Ides of March a famous day in European history because of Brutus, Cassius and a bunch of other Roman dudes.

Did you ever wonder what an "ide" was. Here's the explanation from Wikipedia [Ides of March].

The word Ides comes from the Latin word "Idus" and means "half division" especially in relation to a month. It is a word that was used widely in the Roman calendar indicating the approximate day that was the middle of the month. The term was used for the 15th day of the months of March, May, July, and October, and the 13th day of the other months.

I think you have to be more than 50 years old to appreciate this skit. You might have to be Canadian.1

There's a picture of a yeast (Saccharomyces cerevisiae) ribosome on the cover of the Dec. 16, 2011 issue of Science. The paper inside by Ben-Sham et al. (2011) describes the structure at 3Å resolution.

There's nothing revolutionary here but I thought I would show you the structure just to emphasize a particular point. You can see the same image below without the distracting orange background.

Most of the ribosome is composed of RNA (silver-gray strands). You can see that a lot of this single-stranded RNA forms short double-helical regions when the RNA folds back on itself. Small ribosomal proteins (various colors) decorate the surface of the ribosome by binding to specific regions of the ribosomal RNA.

The overall impression is that the ribosome is a big ball of RNA with a small amount of protein. The actual site of translation, where messenger RNA is translated into a polypeptide, takes place in the middle of the ribosome near the hole you see in this structure. Translation is catalzyed by the RNA component of the ribosome, not by the ribosomal proteins.

I don't know about the rest of you but I grew up with an electron-micrographic image of a ribosome in my head and I just assumed that what I was seeing was a large glob of protein. If course I realized that there was a huge amount or RNA in there somewhere but I didn't think it contributed very much to the dark blobs in the cell.

When the first crystal structures of ribosomes were published I had to stare at them for quite some time in order to purge the old images from my mind and adopt a new perspective.

Eukaryotes have 79 ribosomal proteins and prokaryotic ribosomes have only 52 proteins. There are prokaryotic ribosomal proteins that have no homoogues in eukaryotes and 33 of the eukaryotic ribosomal proteins have no homologues in bacteria—they are eukaryotic specific. Furthermore, many of the eukaryotic proteins differ considerably from their bacterial homologues. (Mostly by extensions of the poly peptide chain.)

The protein components of ribosomes are not highly conserved. One gets the impression that they don't contribute much to the function of a ribosome—an impression confirmed by the fact that the RNA by itself can catalyze polypeptide synthesis. They may help stabilize the three-dimensional structure of the ribosome.

Monday, March 12, 2012

Some species make this molecule for a very special reason. Identify the molecule using the common name and the IUPAC name. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch with a famous Nobel Laureate, or with me if the Nobel Laureate isn't available.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is taurocholate (2-{[(3α,5β,7α,12α)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}ethanesulfonate). Taurocholate is a bile salt in mammals. This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Here's a panoramic view of what it's like to be on the Sandwalk behind Down House (Darwin's Home). This is the stretch along the very back of the property at the top of the image in the header for this blog.

Until two weeks ago, I had been laboring under the naïve assumption that one of the primary goals of every academic was to change students’ beliefs when they were based on inaccurate information. I was awakened from this dogmatic slumber at an interdisciplinary faculty meeting by colleagues who reacted with dismay to my confession that I had tried and failed to disabuse one of my students of Creationist beliefs.

The conversation became more heated when I read to the group what the student had written on her final exam: "I wrote what I had to ‘agree’ with what was said in class, but in truth I believe ABSOLUTELY that there is an amazing, savior GOD, who created the universe, lives among us, and loves us more than anything. That is my ABSOLUTE, and no amount of ‘philosophy’ will change that."

Two of my colleagues, one in the language arts and one in psychology, argued that it was an inappropriate use of my authority to attempt to change this student’s belief; rather, my role should have been to provide her with data so that she could make better decisions.

I countered that both the process that allows one to arrive at Creationist conclusions, and the conclusions themselves, are completely divorced from reality, and that my role was not simply to provide evidence and counterexamples and hope for the best, but to help her overcome a false belief and supplant it with a true one.

Their unanimous reaction to this declaration temporarily made me question one of my basic assumptions about the responsibilities of college educators: Should professors attempt to change students’ beliefs by consistently challenging false beliefs with facts?

I share his frustration. There are far too many university professors who think that the "beliefs" of a student are off limits as long as they have something to do with religion. Those same professors would not hesitate to challenge belief in the superiority of whites over blacks or the efficacy of homeopathy or the validity of supply-side economics.

But it's a different story if a student says that God created the universe 6000 years ago. That belief mustn't be directly challenged because the foolishness of religious beliefs is off limits.

It relates to the idea that science is limited by its insistence on adhering to methodological naturalism. According to this view, science cannot investigate the supernatural. The view is popular among some who oppose creationism since it means that creationism can't be scientific, by fiat. It's also important for accommodationists because it allows science and religion to co-exist in separate magisteria.

I oppose such a definition of science but, up until a few years ago, I was always told that my opinion is irrelevant since all philosophers, and many scientists, agree that science is limited by methodological naturalism. That's why I was so delighted to meet the philosophers from Gent. Finally there was another point of view opposed to the methodological naturalism limitation. Now those who promote this limitation on science have to honestly admit that it's just their opinion and not a universally accepted definition of science.1

According to a widespread philosophical opinion, science is strictly limited to investigating natural causes and putting forth natural explanations. Lacking the tools to evaluate supernatural claims, science must remain studiously neutral on questions of metaphysics. This (self-imposed) stricture, which goes under the name of ‘methodological naturalism’, allows science to be divorced from metaphysical naturalism or atheism, which many people tend to associate with it. However, ruling the supernatural out of science by fiat is not only philosophically untenable, it actually provides grist to the mill of anti-evolutionism. The philosophical flaws in this conception of methodological naturalism have been gratefully exploited by advocates of intelligent design creationism to bolster their false accusations of naturalistic bias and dogmatism on the part of modern science. We argue that it promotes a misleading view of the scientific endeavor and is at odds with the foremost arguments for evolution by natural selection. Reconciling science and religion on the basis of such methodological strictures is therefore misguided.

And here's a brief summary of their position ...

A widespread philosophical opinion conceives of methodological naturalism as an intrinsic and self-imposed limitation of science, as part and parcel of the scientific enterprise by definition. According to this view (Intrinsic Methodological Naturalism or IMN) – which is the official position of both the National Center for Science Education and the National Academy of Sciences and has been adopted in the ruling of Judge John E. Jones III in the Kitzmiller vs. Dover case – science is simply not equipped to deal with the supernatural and hence has no authority on the issue.3

In our view, however, methodological naturalism is a provisory and empirically anchored commitment to naturalistic causes and explanations, which is in principle revocable in light of extraordinary evidence (Provisory or Pragmatic Methodological Naturalism – PMN). Methodological naturalism thus conceived derives its rationale from the impressive dividends of naturalistic explanations and the consistent failure of supernatural explanations throughout the history of science.4

The distinction between Intrinsic Methodological naturalism (IMN) and Pragmatic Methodological Naturalism (PMN) is important. PMN is a conclusion based on centuries of scientific evidence strongly suggesting that natural explanations are sufficient to explain all phenomena. Those investigations include looking onto possible supernatural explanations.

Scientists have actually investigated possible miracles and found no evidence for them. Scientist have actually investigated the supernatural explanation for a world-wide deluge and refuted it. And if someone says that God made bacterial flagella, real scientists will try and find out whether that's true instead of just throwing up their hands and claiming that such an explanation is outside of science.

The implications of PMN are profound. It means that science and religion really are in conflict.

1. Of course the accommodationists will admit no such thing as I'm sure you are about to see in the comments. Such an admission would require them to say that they mislead Judge Jones in the Dover trial.

Wednesday, March 07, 2012

Yesterday I was talking to one of my colleagues and she asked me if I'd heard the latest news about the Burgess Shale. I confessed ignorance so she told me that scientists had just discovered a primitive vertebrate fossil in the Burgess Shale.

Hmmm ... I was aware of possible primitive vertebrates ("Craniates" is a better term) in the deposits from China (e.g. Myllokunmingia) but I'd never heard of a vertebrate fossil in the Burgess Shale so I thought I'd check out the press release.

Researchers from the University of Toronto, the Royal Ontario Museum (ROM) and the University of Cambridge have confirmed that a 505 million-year-old creature, found only in the Burgess Shale fossil beds in Canada’s Yoho National Park, is the most primitive known vertebrate and therefore the ancestor of all descendant vertebrates, including humans.

The research team’s analysis proves the extinct Pikaia gracilens is the most primitive member of the chordate family, the group of animals that today includes fish, amphibians, birds, reptiles and mammals. Their study is based on the analysis of 114 specimens and is published in the British scientific journal Biological Reviews.

“The discovery of myomeres is the smoking gun that we have long been seeking,” said the study’s lead author, Professor Simon Conway Morris of the University of Cambridge. “Now with myomeres, a nerve chord, a notochord and a vascular system all identified, this study clearly places Pikaia as the planet’s most primitive chordate. So, next time we put the family photograph on the mantle-piece, there in the background will be Pikaia."

Furthermore, this really isn't news. Pikaia was featured in Stephen Jay Gould's book Wonderful Life published in 1989. Even then, Pikaia gracilens was thought to be a chordate similar in broad features to the cephalochordate (non-vertebrate chordate) Amphioxus. This classification was attributed to Simon Conway Morris in 1979. The Wikipedia article [Pikaia] points out that this classification was not universally accepted.

The important points are: (1) that Pikaia is a primitive chordate but not a primitive vertebrate and the press release is just dead wrong about that and, (2) this is old news.

BTW, is Conway-Morris right about Pikaia being the oldest chordate? I thought the fossils from China were older and some of those might even be vertebrates. If that's true then Pikaia lived after the divergence of cephalochordates and vertebrates and it's not even remotely possible that it's our ancestor.

There ought to be a new rule about press releases. Each one should have a statement at the end saying the the press release has been read by the authors of the study and they approve its content.

Until a few minutes ago I had never heard of "redshirting" although I was familiar with the concept. Some parents want to hold their children back from kindergarten (or have them repeat kindergarten) so they will be older and more mature than the other students in their class. A school teacher advised us to do that for one of our children but we adamantly refused. Best decision we ever made concerning the education of our children.

When I was growing up the best and brightest students were allowed to skip a grade if they were doing well. (I took grades three and four in a single year.) It was a mark of achievement to be among the youngest in your class, especially if you were doing as well, or better, than the other students. On the other hand, if you were the oldest in the class then your achievements were discounted because you had an intrinsic advantage.

When I was growing up it would have been psychologically devastating to be the oldest student in the class and not be at the top of the class academically. (That's partly because the oldest students were usually the ones who had flunked a grade.) I wonder if parents who hold their children back have ever thought about the potential negative consequences? What happens if your child is just average and redshirting doesn't work?

Here's a 60 Minutes segment on redshirting. It features two people from the University of Toronto: writer Malcolm Gladwell (B.A. 1984, Trinity College) and economist Elizabeth Dhuey a professor in the Department of Management.

Tuesday, March 06, 2012

This month's Carnival of Evolution (45th version) is hosted by Adrian, a Canadian from Edmonton, Alberta who blogs at Splendor Awaits: Carnival of Evolution #45.

Here at last is the Carnival of Evolution. Because there were so few bug-based submissions, I had to change my plans and think of a new approach. I decided this would be a good time to try the new Google Presentation. This plays for me in the latest edition of Firefox, let me know how it works on your browser.

On with the Carnival! It’s awkward, a bit goofy and tongue-in-cheeky, but it does have bugs.

The next Carnival of Evolution (April) needs a host. Contact Bjørn Østman at Carnival of Evolution if you want to volunteer. Meanwhile, you can submit your articles for next month's carnival at Carnival of Evolution.

Helena Curtis was an amazing writer. She's famous for her introductory biology textbook published by Worth beginning in 1968 [Good Science Writers: Helena Curtis]. Here's the opening paragraphs.

Our universe began, according to current theory, with an explosion that filled all space, with every particle of matter hurled away from every other particle. The temperature at the time of the explosion—some 10 to 20 billion years ago—was about 100,000000000 degrees Celsius (1011 °C). At this temperature, not even atoms could hold together; all matter was in the form of subatomic, elementary particles. Moving at enormous velocities, even those particles had fleeting lives. Colliding with great force, they annihilated one another, creating new particles and releasing great energy.

As the universe cooled, two types of stable particles, previously present only in relatively small amounts, began to assemble. (By this time, several hundred thousand years after the "big bang" is believed to have taken place, the temperature had dropped to a mere 2500°C, about the temperature of white-hot wire in an incandescent light bulb.) These particles—protons and neutrons—are very heavy as subatomic particles go. Held together by forces that are still incompletely understood, they formed the central cores, or nuclei, of atoms. These nuclei, with their positively charged protons, attracted small, light, negatively charged particles—electrons—which moved rapidly around them. Thus, atoms came into being.

It is from these atoms—blown apart, formed, and re-formed over the course of several billion years—that all the stars and planets of our universe are formed, including our particular star and planet. And it is from the atoms present on this planet that living systems assembled themselves and evolved. Each atom in our own bodies had its origin in that enormous explosion 10 to 20 billion years ago. You and I are flesh and blood, but we are also stardust.

Neil DeGrasse Tyson tops that in his spontaneous answer to the question, "What is the most astounding fact you can share with us about the Universe?"

If you're going to sing "we are stardust" then you can't do it any better than this group. The song was written by Joni Mitchell (another Canadian) but her version is not as good.

Monday, March 05, 2012

I saw this portrait in the Huntington Library in San Marino (near Pasedena) California, USA. This man was the friend of a kite flyer, a pottery maker, and Erasmus Darwin. One of Ms. Sandwalk's direct ancestors worked for him.

He's very famous. You'll recognize the name instantly even if you don't recognize his face. Who is he?

I'll keep the comments invisible for 24 hours so you can post your guesses.

This is a very important molecule for some species. It's important to me, for example, because I worked with it in an undergraduate research project forty-nine many years ago.

UPDATE: The original structure was missing a methyl group at the bottom right. This has now been corrected.

Identify the molecule—the common name will do but make sure you get it right because there are quite a few similar molecules. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisable for 24 hours. Comments are now open.

UPDATE: The molecule is a gibberellin-like molecule. It was intended to be gibberellin GA1 but I left off a methyl group. This is similar to Monday's Molecule #102 (gibberellin GA3). Defects in one of the genes for gibberellin GA1 synthesis gave rise to the tall/short phenotype studied by Gregor Mendel [Mendel's Stem Length Gene (Le)]. Gibberellin GA1 was one of the molecules synthesized by Elias James Corey, winner of the Nobel Prize in Chemistry 1990. The winner this week is Albi Celaj.

The Centre for Inquiry (Toronto) is trying to get back on track after CFI fired two National Executive Directors and the director of CFI Ontario/Toronto. We've lost our facility on Beverley Street so we now have to meet at various other locations in different parts of the city.

During the 1980s he stimulated people's temporal lobes artificially with a weak magnetic field to see if he could induce a religious state (see God helmet). He claimed that the field could produce the sensation of "an ethereal presence in the room". This research has received wide coverage in the media, with high profile visitors to Persinger's lab Susan Blackmore and Richard Dawkins reporting positive[8] and negative[9] results respectively.

The only published attempt, by a research group in Sweden, to replicate these effects failed to do so and concluded that subjects' reports correlated with their personality characteristics and suggestibility. They also criticised Persinger for insufficient double-blinding.[10] Persinger responded that the Swedish group had an incorrect computer setup,[11] a claim that the Swedish group dispute,[12] and that many of his previous experiments were indeed carried out double-blind,[13] although the Swedish group have also disputed this.[12]

Persinger is also famous for suggesting that "extremely low-frequency (ELF) electromagnetic waves may be able to carry telepathic and clairvoyant information" and for his "1975 Tectonic Strain Theory (TST) of how geophysical variables may correlate with sightings of unidentified flying objects (UFOs) or Marian apparitions." He also claims that women are far more susceptible to his God Helmet than men [Evolution Makes Women Stupid].

Here's your chance to meet Michael Persinger on Friday March 9, 2012 at York University. The Centre for Inquiry is co-sponsoring the event.

What if we could recreate a religious experience by simply flipping a switch in the brain? What if we could produce the feeling that someone or something is watching over us on demand? According to neuroscientific research conducted with The God Helmet, this may be possible.

The God Helmet, invented by Stanley Koren and used primarily by Dr. Michael Persinger, has forced us to reconsider the neurological basis of religion in the brain. The headgear is controversial because when electromagnetic waves are sent through a subject's temporal lobe, it can create the feeling of a religious experience, or a sense of belonging. “We basically imitate what happens within the brain itself during a mystical experience,” says Dr. Persinger.

In this engaging lecture with guest speakers Trevor Carniello and Dr. Michael Persinger, learn about how The God Helmet works and discover the origin of religious experiences in the brain. Join us in this exclusive opportunity to be able to ask Dr. Persinger questions and find answers to your curiosities about God, the brain and religion.

The lecture takes place on Friday, March 9th at York University. Tickets are available at freesay.wordpress.com. This event is brought to you by Free[SAY]: Freethinkers, Skeptics and Atheists at York in collaboration with the Center For Inquiry.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.